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- PDB-4bbg: Crystal structure of human kinesin Eg5 in complex with 3-(((2-Ami... -

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Basic information

Entry
Database: PDB / ID: 4bbg
TitleCrystal structure of human kinesin Eg5 in complex with 3-(((2-Aminoethyl)sulfanyl)(3-ethylphenyl) phenylmethyl)phenol
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsCELL CYCLE / MITOSIS / INHIBITOR
Function / homology
Function and homology information


spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-V02 / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKaan, H.Y.K. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Optimized S-Trityl-L-Cysteine-Based Inhibitors of Kinesin Spindle Protein with Potent in Vivo Antitumor Activity in Lung Cancer Xenograft Models.
Authors: Good, J.A.D. / Wang, F. / Rath, O. / Kaan, H.Y.K. / Talapatra, S.K. / Podgorski, D. / Mackay, S.P. / Kozielski, F.
History
DepositionSep 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0489
Polymers41,0561
Non-polymers9928
Water1,67593
1
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules

A: KINESIN-LIKE PROTEIN KIF11
hetero molecules

A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,14427
Polymers123,1673
Non-polymers2,97724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
Buried area8010 Å2
ΔGint-174.1 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.190, 158.190, 158.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 1 molecules A

#1: Protein KINESIN-LIKE PROTEIN KIF11 / / KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HKSP / KINESIN-RELATED MOTOR PROTEIN EG5 / ...KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HKSP / KINESIN-RELATED MOTOR PROTEIN EG5 / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5


Mass: 41055.582 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1 - 368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P52732

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Non-polymers , 5 types, 101 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-V02 / 3-[(R)-2-azanylethylsulfanyl-(3-ethylphenyl)-phenyl-methyl]phenol


Mass: 363.516 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25NOS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.44 % / Description: NONE
Crystal growpH: 5.5
Details: 22 % POLYETHYLENE GLYCOL-3350, 0.3 M AMMONIUM SULPHATE, 0.1 M MES PH 5.5 AND 0.01 M TRIMETHYLAMINE HYDROCHLORIDE

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 17253 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KEN

3ken


Resolution: 2.75→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.799 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22964 874 5.1 %RANDOM
Rwork0.18248 ---
obs0.18491 16379 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.846 Å2
Refinement stepCycle: LAST / Resolution: 2.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 59 93 2770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222730
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.9933704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.195338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6224.237118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23915487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7961520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212008
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.51677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28222729
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.18631053
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6034.5973
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 66 -
Rwork0.217 1212 -
obs--100 %

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